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- PDB-2f32: Xray crystal structure of lysozyme mutant L20/R63A liganded to et... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2f32 | ||||||
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Title | Xray crystal structure of lysozyme mutant L20/R63A liganded to ethylguanidinium | ||||||
![]() | Lysozyme | ||||||
![]() | HYDROLASE / MOLECULAR SWITCH / T4 LYSOZYME / NANO-BITECHNOLOGY / PROTEIN ENGINEERING / PROTEIN DESIGN | ||||||
Function / homology | ![]() viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yousef, M.S. / Bischoff, N. / Dyer, C.M. / Baase, W.A. / Matthews, B.W. | ||||||
![]() | ![]() Title: Guanidinium derivatives bind preferentially and trigger long-distance conformational changes in an engineered T4 lysozyme. Authors: Yousef, M.S. / Bischoff, N. / Dyer, C.M. / Baase, W.A. / Matthews, B.W. #1: ![]() Title: Use of Sequence Duplication to Engineer a Ligand-Triggered, Long-Distance Molecular Switch in T4 Lysozyme. Authors: Yousef, M.S. / Baase, W.A. / Matthews, B.W. #2: ![]() Title: Structural Characterization of an Engineered Tandem Repeat Contrasts the Importance of Context and Sequence in Protein Folding. Authors: Sagermann, M. / Baase, W.A. / Matthews, B.W. #3: ![]() Title: Long-Distance Conformational Changes in a Protein Engineered by Modulated Sequence Duplication Authors: Sagermann, M. / Gay, L. / Matthews, B.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 53.4 KB | Display | ![]() |
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PDB format | ![]() | 37.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.5 KB | Display | ![]() |
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Full document | ![]() | 453.5 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 16.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2f2qC ![]() 2f47C ![]() 1t8aS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19685.541 Da / Num. of mol.: 1 / Mutation: L39I, INS (NAAKSELDKAI -N62), R63A, C65T, C108A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-BME / |
#3: Chemical | ChemComp-EGD / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.8 M MIXED POTASSIUM AND SODIUM PHOSPHATE. 0.2 M ETHYL GUANIDINIUM CHLORIDE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. obs: 19758 / % possible obs: 99 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.07 / Net I/σ(I): 28 |
Reflection shell | Resolution: 1.8→1.86 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.36 / % possible all: 99 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1T8A Resolution: 1.8→27.38 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 569234.74 / Data cutoff high rms absF: 569234.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.4182 Å2 / ksol: 0.348392 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→27.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.91 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
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Xplor file |
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